Torsional Diffusion for Molecular Conformer Generation

1 June 2022

Papers citing "Torsional Diffusion for Molecular Conformer Generation"

50 / 169 papers shown

Title
Equivariant flow matching Leon Klein Andreas Krämer Frank Noé 16 59 0 26 Jun 2023
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation Danny Reidenbach Aditi S. Krishnapriyan 27 7 0 26 Jun 2023
Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials Shengchao Liu Weitao Du Yanjing Li Zhuoxinran Li Zhiling Zheng ... Anima Anandkumar C. Borgs J. Chayes Hongyu Guo Jian Tang AI4CE 31 19 0 15 Jun 2023
InfoDiffusion: Representation Learning Using Information Maximizing Diffusion Models Yingheng Wang Yair Schiff Aaron Gokaslan Weishen Pan Fei Wang Chris De Sa Volodymyr Kuleshov DiffM 14 39 0 14 Jun 2023
Hyperbolic Graph Diffusion Model Lingfeng Wen Xuan Tang Mingjie Ouyang Xiangxiang Shen Jian Yang Daxin Zhu Mingsong Chen Xian Wei 31 2 0 13 Jun 2023
3D molecule generation by denoising voxel grids Pedro H. O. Pinheiro Joshua Rackers J. Kleinhenz Michael R. Maser Omar Mahmood Andrew Watkins Stephen Ra Vishnu Sresht Saeed Saremi DiffM 34 20 0 13 Jun 2023
Von Mises Mixture Distributions for Molecular Conformation Generation K. Swanson Jake Williams Eric Jonas 22 6 0 13 Jun 2023
Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling Jiarui Lu Bozitao Zhong Zuobai Zhang Jian Tang 19 24 0 05 Jun 2023
Extracting Reward Functions from Diffusion Models Felipe Nuti Tim Franzmeyer João F. Henriques 19 14 0 01 Jun 2023
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing Yang Zhang Zuobai Zhang Bozitao Zhong Sanchit Misra Jian Tang DiffM 16 31 0 01 Jun 2023
Implicit Transfer Operator Learning: Multiple Time-Resolution Surrogates for Molecular Dynamics M. Schreiner Ole Winther Simon Olsson OOD AI4CE 38 13 0 29 May 2023
Learning to Jump: Thinning and Thickening Latent Counts for Generative Modeling Tianqi Chen Mingyuan Zhou DiffM 52 7 0 28 May 2023
Manifold Diffusion Fields Ahmed A. A. Elhag Yuyang Wang J. Susskind Miguel Angel Bautista DiffM AI4CE 36 4 0 24 May 2023
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design Zaixin Zhang Qi Liu 25 34 0 22 May 2023
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation Han Huang Leilei Sun Bowen Du Weifeng Lv DiffM 16 16 0 21 May 2023
CREMP: Conformer-Rotamer Ensembles of Macrocyclic Peptides for Machine Learning Colin A. Grambow Hayley Weir Christian N Cunningham Tommaso Biancalani Kangway V Chuang 18 4 0 14 May 2023
A Latent Diffusion Model for Protein Structure Generation Cong Fu Keqiang Yan Limei Wang Wing Yee Au Michael McThrow Tao Komikado Koji Maruhashi Kanji Uchino Xiaoning Qian Shuiwang Ji DiffM 13 31 0 06 May 2023
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D Bo Qiang Yuxuan Song Minkai Xu Jingjing Gong B. Gao Hao Zhou Weiying Ma Yanyan Lan DiffM 38 18 0 05 May 2023
Diffusion-based Generative AI for Exploring Transition States from 2D Molecular Graphs Seonghwan Kim Jeheon Woo Woo Youn Kim DiffM 30 25 0 20 Apr 2023
SpectralDiff: A Generative Framework for Hyperspectral Image Classification with Diffusion Models Ning Chen Jun Yue Leyuan Fang Shaobo Xia DiffM 25 57 0 12 Apr 2023
Diffusion Models for Constrained Domains N. Fishman Leo Klarner Valentin De Bortoli Emile Mathieu M. Hutchinson DiffM 20 35 0 11 Apr 2023
Reflected Diffusion Models Aaron Lou Stefano Ermon 24 49 0 10 Apr 2023
DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models Mohamed Amine Ketata Cedrik Laue R. Mammadov Hannes Stärk Menghua Wu Gabriele Corso Ćeline Marquet Regina Barzilay Tommi Jaakkola 18 46 0 08 Apr 2023
Neural Diffeomorphic Non-uniform B-spline Flows S. Hong S. Chun 27 1 0 07 Apr 2023
EigenFold: Generative Protein Structure Prediction with Diffusion Models Bowen Jing Ezra Erives Peter Pao-Huang Gabriele Corso Bonnie Berger Tommi Jaakkola DiffM 20 66 0 05 Apr 2023
A Survey on Graph Diffusion Models: Generative AI in Science for Molecule, Protein and Material Mengchun Zhang Maryam Qamar Taegoo Kang Yuna Jung Chenshuang Zhang Sung-Ho Bae Chaoning Zhang DiffM MedIm 31 44 0 04 Apr 2023
DiffTAD: Temporal Action Detection with Proposal Denoising Diffusion Sauradip Nag Xiatian Zhu Jiankang Deng Yi-Zhe Song Tao Xiang DiffM VGen 28 21 0 27 Mar 2023
Infinite Physical Monkey: Do Deep Learning Methods Really Perform Better in Conformation Generation? Haotian Zhang Jintu Zhang Huifeng Zhao Dejun Jiang Yafeng Deng 22 1 0 08 Mar 2023
Chemically Transferable Generative Backmapping of Coarse-Grained Proteins Soojung Yang Rafael Gómez-Bombarelli AI4CE 30 16 0 02 Mar 2023
Denoising Diffusion Samplers Francisco Vargas Will Grathwohl Arnaud Doucet DiffM 19 75 0 27 Feb 2023
Internal-Coordinate Density Modelling of Protein Structure: Covariance Matters Marloes Arts J. Frellsen Wouter Boomsma 31 0 0 27 Feb 2023
PrefixMol: Target- and Chemistry-aware Molecule Design via Prefix Embedding Zhangyang Gao Yuqi Hu Cheng Tan Stan Z. Li 26 13 0 14 Feb 2023
Do Deep Learning Methods Really Perform Better in Molecular Conformation Generation? G. Zhou Zhifeng Gao Zhewei Wei Hang Zheng Guolin Ke OOD AI4CE BDL 25 15 0 14 Feb 2023
Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action Zhiye Guo Jian Liu Yanli Wang Mengrui Chen Duolin Wang Dong Xu Jianlin Cheng MedIm AI4CE DiffM 46 22 0 13 Feb 2023
Generative Diffusion Models on Graphs: Methods and Applications C. Liu Wenqi Fan Yunqing Liu Jiatong Li Hang Li Hui Liu Jiliang Tang Qing Li MedIm DiffM 26 57 0 06 Feb 2023
SE(3) diffusion model with application to protein backbone generation Jason Yim Brian L. Trippe Valentin De Bortoli Emile Mathieu Arnaud Doucet Regina Barzilay Tommi Jaakkola DiffM 12 194 0 05 Feb 2023
Timewarp: Transferable Acceleration of Molecular Dynamics by Learning Time-Coarsened Dynamics Leon Klein Andrew Y. K. Foong T. E. Fjelde Bruno Mlodozeniec Marc Brockschmidt Sebastian Nowozin Frank Noé Ryota Tomioka AI4CE 27 42 0 02 Feb 2023
Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics Marloes Arts Victor Garcia Satorras Chin-Wei Huang Daniel Zuegner Marco Federici C. Clementi Frank Noé Robert Pinsler Rianne van den Berg DiffM 11 85 0 01 Feb 2023
ERA-Solver: Error-Robust Adams Solver for Fast Sampling of Diffusion Probabilistic Models Shengmeng Li Luping Liu Zenghao Chai Runnan Li Xuejiao Tan DiffM 22 11 0 30 Jan 2023
A theory of continuous generative flow networks Salem Lahlou T. Deleu Pablo Lemos Dinghuai Zhang Alexandra Volokhova Alex Hernández-García Léna Néhale Ezzine Yoshua Bengio Nikolay Malkin AI4CE 28 79 0 30 Jan 2023
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction Zuobai Zhang Minghao Xu A. Lozano Vijil Chenthamarakshan Payel Das Jian Tang DiffM 11 19 0 28 Jan 2023
DiffSDS: A language diffusion model for protein backbone inpainting under geometric conditions and constraints Zhangyang Gao Cheng Tan Stan Z. Li DiffM 21 19 0 22 Jan 2023
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation Han Huang Leilei Sun Bowen Du Weifeng Lv 29 40 0 01 Jan 2023
Uncovering the Disentanglement Capability in Text-to-Image Diffusion Models Qiucheng Wu Yujian Liu Handong Zhao Ajinkya Kale T. Bui Tong Yu Zhe-nan Lin Yang Zhang Shiyu Chang DiffM CoGe 19 97 0 16 Dec 2022
Latent Space Diffusion Models of Cryo-EM Structures Karsten Kreis Tim Dockhorn Zihao Li Ellen D. Zhong DiffM 27 15 0 25 Nov 2022
HouseDiffusion: Vector Floorplan Generation via a Diffusion Model with Discrete and Continuous Denoising M. Shabani Sepidehsadat Hosseini Yasutaka Furukawa DiffM 21 58 0 23 Nov 2022
DiffusionDet: Diffusion Model for Object Detection Shoufa Chen Pei Sun Yibing Song Ping Luo 44 442 0 17 Nov 2022
An optimal control perspective on diffusion-based generative modeling Julius Berner Lorenz Richter Karen Ullrich DiffM 23 80 0 02 Nov 2022
The Open MatSci ML Toolkit: A Flexible Framework for Machine Learning in Materials Science Santiago Miret Kin Long Kelvin Lee Carmelo Gonzales Marcel Nassar Matthew Spellings 27 19 0 31 Oct 2022
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lió Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 29 193 0 24 Oct 2022